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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        About MultiQC

        This report was generated using MultiQC, version 1.30

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-07-28, 16:44 CEST based on data in: /mnt/c/Users/Yun Wang/Ubuntu_share/0d4fdc6fe762bc83d8eef766094163

        Number of samples

        Total number of local vs. external samples.

        Showing 2/2 rows.
        sample_typecount
        External
        2
        Local
        8

        Count Quality Control - Read Counts

        Count Quality Control - Mapped vs Counted Reads

        Compares total mapped vs counted reads.

        The Mapped vs Counted Reads plot does not include external counts.

        Consider removing samples with too low or too high size factors.

        Count Quality Control - Size Factors

        Reads Summary Statistics

        Showing 10/10 rows and 3/3 columns.
        RNA_IDReads MappedReads CountedSize Factors
        HG00106
        63542
        39291
        1.0
        HG00111
        77674
        49223
        1.1
        HG00116
        61360
        38422
        0.9
        HG00126
        72929
        44651
        1.0
        HG00132
        79999
        49977
        1.2
        HG00149
        66002
        39384
        0.9
        HG00150
        71699
        45629
        1.0
        HG00176
        60056
        37036
        0.8
        HG00178
        NA
        212402
        1.2
        HG00181
        NA
        171356
        0.8

        Filtering

        Filtering local: A pre-filtered summary of counts using only the local (from BAM) counts. Omitted if no external counts

        all: A pre-filtered summary of counts using only the merged local (from BAM) and external counts

        passed FPKM: Passes the user defined FPKM cutoff in at least 5% of genes

        min 1 read: minimum of 1 read expressed in 5% of genes

        min 10 reads: minimum of 10 reads expressed in 5% of genes.

        Expressed Genes

        Expressed Genes - table

        Showing 10/10 rows and 6/6 columns.
        RNA_IDRankExpressed genesUnion of expressed genesIntersection of expressed genesGenes passed filteringIs External
        HG00106
        8
        125
        155
        96
        155
        FALSE
        HG00111
        6
        122
        147
        99
        147
        FALSE
        HG00116
        1
        112
        112
        112
        112
        FALSE
        HG00126
        5
        120
        141
        99
        141
        FALSE
        HG00132
        3
        119
        132
        101
        132
        FALSE
        HG00149
        7
        124
        151
        96
        151
        FALSE
        HG00150
        4
        119
        139
        100
        139
        FALSE
        HG00176
        2
        114
        123
        103
        123
        FALSE
        HG00178
        10
        341
        391
        95
        391
        TRUE
        HG00181
        9
        328
        360
        96
        360
        TRUE

        Sample Sex Annotation

        Considerations:The verifying of the samples sex is performed by comparing the expression levels of the genes XIST and UTY. In general, females should have high XIST and low UTY expression, and viceversa for males. For it to work, the sample annotation must have a column called ‘SEX’, with values male/female. If some other values exist, e.g., unknown, they will be matched. The prediction is performed via a linear discriminant analysis on the log2 counts.

        Sex column not found in sample annotation

        MultiQC v1.30 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.